| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-proline catabolism | proV | hi | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 54% | 99% | 410.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 49% | 381.3 |
| L-proline catabolism | opuBA | med | BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) | 49% | 95% | 356.3 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-histidine catabolism | hutV | med | ABC transporter for L-Histidine, ATPase component (characterized) | 59% | 96% | 311.6 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-proline catabolism | hutV | med | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 57% | 96% | 302.8 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 72% | 173.3 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 72% | 173.3 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 72% | 173.3 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 72% | 173.3 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 72% | 173.3 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 72% | 173.3 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| D-maltose catabolism | malK1 | lo | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 39% | 62% | 172.9 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| trehalose catabolism | thuK | lo | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 39% | 62% | 172.9 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 37% | 67% | 171 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 38% | 66% | 168.7 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 41% | 59% | 168.3 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 41% | 65% | 164.9 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 39% | 60% | 162.9 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 37% | 70% | 161.4 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 37% | 61% | 159.1 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| D-mannose catabolism | TT_C0211 | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 36% | 70% | 159.1 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| sucrose catabolism | thuK | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 36% | 70% | 159.1 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 31% | 99% | 158.7 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 31% | 99% | 158.7 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-arginine catabolism | artP | lo | Histidine transport ATP-binding protein HisP (characterized) | 36% | 95% | 157.9 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-histidine catabolism | hisP | lo | Histidine transport ATP-binding protein HisP (characterized) | 36% | 95% | 157.9 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-lysine catabolism | hisP | lo | Histidine transport ATP-binding protein HisP (characterized) | 36% | 95% | 157.9 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 32% | 92% | 156.8 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 36% | 62% | 156 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 34% | 76% | 154.1 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 39% | 91% | 153.7 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 39% | 91% | 153.7 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-glutamate catabolism | gltL | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 39% | 91% | 153.7 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 34% | 82% | 152.9 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 85% | 152.5 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 85% | 152.5 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 35% | 80% | 152.5 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 36% | 60% | 151.8 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 39% | 77% | 151 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 34% | 69% | 150.6 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 35% | 98% | 150.2 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 35% | 98% | 149.8 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 35% | 97% | 148.3 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-asparagine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 37% | 87% | 146.4 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-aspartate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 37% | 87% | 146.4 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-glutamate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 37% | 87% | 146.4 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-leucine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 37% | 87% | 146.4 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-proline catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 37% | 87% | 146.4 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-asparagine catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 34% | 99% | 145.2 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-aspartate catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 34% | 99% | 145.2 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 37% | 81% | 139.8 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
| L-citrulline catabolism | PS417_17605 | lo | ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) | 34% | 89% | 129.8 | Glycine betaine/choline transport system ATP-binding protein OusV | 54% | 418.3 |
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using
ublast (a fast alternative to protein BLAST)
against a database of manually-curated proteins (most of which are experimentally characterized) or by using
HMMer with enzyme models (usually from
TIGRFam). Ublast hits may be split across two different proteins.
Steps with no high- or medium-confidence candidates may be considered "gaps."
For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways.
For diverse bacteria and archaea that can utilize a carbon source, there is a complete
high-confidence catabolic pathway (including a transporter) just 38% of the time, and
there is a complete medium-confidence pathway 63% of the time.
Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know